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Title: Prospects and challenges for fungal metatranscriptomes of complex communities

Journal Article · · Fungal Ecology
 [1];  [1];  [1]; ORCiD logo [2];  [3];  [1];  [4];  [5]
  1. Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Bioscience Division
  2. Michigan State Univ., East Lansing, MI (United States). Dept. of Microbiology and Molecular Genetics
  3. Univ. of Wisconsin, Madison, WI (United States). United States Department of Agriculture, Forest Products Lab.
  4. Concordia Univ., Montreal, QC (Canada). Centre for Structural and Functional Genomics
  5. Duke Univ., Durham, NC (United States). Biological Sciences
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We report that the ability to extract and purify messenger RNA directly from plants, decomposing organic matter and soil, followed by high-throughput sequencing of the pool of expressed genes, has spawned the emerging research area of metatranscriptomics. Each metatranscriptome provides a snapshot of the composition and relative abundance of actively transcribed genes, and thus provides an assessment of the interactions between soil microorganisms and plants, and collective microbial metabolic processes in many environments. We highlight current approaches for analysis of fungal transcriptome and metatranscriptome datasets across a gradient of community complexity, and note benefits and pitfalls associated with those approaches. Finally, we discuss knowledge gaps that limit our current ability to interpret metatranscriptome datasets and suggest future research directions that will require concerted efforts within the scientific community.

Research Organization:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER)
Grant/Contract Number:
AC52-06NA25396; 2014LANLF260; LA-UR-14-28371
OSTI ID:
1329856
Alternate ID(s):
OSTI ID: 1357068
Report Number(s):
LA-UR-14-28371
Journal Information:
Fungal Ecology, Vol. 14; ISSN 1754-5048
Publisher:
ElsevierCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 35 works
Citation information provided by
Web of Science

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Cited By (12)

The role of locally adapted mycorrhizas and rhizobacteria in plant-soil feedback systems journal April 2016
Biology and Ecology of Freshwater Fungi book January 2016
Fungal ecological strategies reflected in gene transcription ‐ a case study of two litter decomposers journal August 2019
The pitfalls of biodiversity proxies: Differences in richness patterns of birds, trees and understudied diversity across Amazonia journal December 2019
A simple pyrocosm for studying soil microbial response to fire reveals a rapid, massive response by Pyronema species posted_content September 2019
Anthropogenic N deposition, fungal gene expression, and an increasing soil carbon sink in the Northern Hemisphere journal July 2019
Mycobiome diversity: high-throughput sequencing and identification of fungi journal November 2018
Gene expression of indoor fungal communities under damp building conditions: Implications for human health journal April 2018
Metatranscriptomics as a tool to identify fungal species and subspecies in mixed communities – a proof of concept under laboratory conditions journal August 2019
Fungal endophytes: modifiers of plant disease journal December 2015
A simple pyrocosm for studying soil microbial response to fire reveals a rapid, massive response by Pyronema species journal March 2020
Forest floor community metatranscriptomes identify fungal and bacterial responses to N deposition in two maple forests journal April 2015

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
54 ENVIRONMENTAL SCIENCES
Environmental RNA
Fungal metabolism
Fungal transcriptome
K-mer
Metatranscriptome
Sequence databases